Arbidol monotherapy is superior to lopinavir/ritonavir in treating COVID-19

Lopinavir/ritonavir and arbidol have been previously used to treat acute respiratory syndrome- coronavirus 2 (SARS-CoV-2) replication in clinical practice; nevertheless, their effectiveness remains controversial. In this study, we evaluated the antiviral effects and safety of lopinavir/ritonavir and arbidol in patients with the 2019-nCoV disease (COVID-19). Fifty patients with laboratory-confirmed COVID-19 were divided into two groups: including lopinavir/ritonavir group (34 cases) and arbidol group (16 cases). Lopinavir/ritonavir group received 400 mg/100mg of Lopinavir/ritonavir, twice a day for a week, while the arbidol group was given 0.2 g arbidol, three times a day. Data from these patients were retrospectively analyzed. The cycle threshold values of open reading frame 1ab and nucleocapsid genes by RT-PCR assay were monitored during antiviral therapy. None of the patients developed severe pneumonia or ARDS. There was no difference in fever duration between the two groups (P=0.61). On day 14 after the admission, no viral load was detected in arbidol group, but the viral load was found in 15(44.1%) patients treated with lopinavir/ritonavir. Patients in the arbidol group had a shorter duration of positive RNA test compared to those in the lopinavir/ritonavir group (P<0.01). Moreover, no apparent side effects were found in both groups. In conclusion, our data indicate that arbidol monotherapy may be superior to lopinavir/ritonavir in treating COVID-19.

Novel Yersinia enterocolitica Prophages and a Comparative Analysis of Genomic Diversity

Yersinia enterocolitica is a major agent of foodborne diseases worldwide. Prophage plays an important role in the genetic evolution of the bacterial genome. Little is known about the genetic information about prophages in the genome of Y. enterocolitica, and no pathogenic Y. enterocolitica prophages have been described. In this study, we induced and described the genomes of six prophages from pathogenic Y. enterocolitica for the first time. Phylogenetic analysis based on whole genome sequencing revealed that these novel Yersinia phages are genetically distinct from the previously reported phages, showing considerable genetic diversity. Interestingly, the prophages induced from O:3 and O:9 Y. enterocolitica showed different genomic sequences and morphology but highly conserved among the same serotype strains, which classified into two diverse clusters. The three long-tailed Myoviridae prophages induced from serotype O:3 Y. enterocolitica were highly conserved, shared ≥99.99% identity and forming genotypic cluster A; the three Podoviridae prophages induced from the serotype O:9 strains formed cluster B, also shared more than 99.90% identity with one another. Cluster A was most closely related to O:5 non-pathogenic Y. enterocolitica prophage PY54 (61.72% identity). The genetic polymorphism of these two kinds of prophages and highly conserved among the same serotype strains, suggested a possible shared evolutionary past for these phages: originated from distinct ancestors, and entered pathogenic Y. enterocolitica as extrachromosomal genetic components during evolution when facing selective pressure. These results are critically important for further understanding of phage roles in host physiology and the pathology of disease.

DTDP-rhamnosyl transferase RfbF, is a newfound receptor-related regulatory protein for phage phiYe-F10 specific for Yersinia enterocolitica serotype O:3

Bacteriophages and their hosts are continuously engaged in evolutionary competition. Here we isolated a lytic phage phiYe-F10 specific for Yersinia enterocolitica serotype O:3. We firstly described the phage receptor was regulated by DTDP-rhamnosyl transferase RfbF, encoded within the rfb cluster that was responsible for the biosynthesis of the O antigens. The deletion of DTDP-rhamnosyl transferase RfbF of wild type O:3 strain caused failure in phiYe-F10 adsorption; however, the mutation strain retained agglutination with O:3 antiserum; and complementation of its mutant converted its sensitivity to phiYe-F10. Therefore, DTDP-rhamnosyl transferase RfbF was responsible for the phage infection but did not affect recognition of Y. enterocolitica O:3 antiserum. Further, the deletions in the putative O-antigen biosynthesis protein precursor and outer membrane protein had no effect on sensitivity to phiYe-F10 infection. However, adsorption of phages onto mutant HNF10-ΔO-antigen took longer time than onto the WT, suggesting that deletion of the putative O-antigen biosynthesis protein precursor reduced the infection efficiency.

[Detection of Yersinia Enterocolitica Bacteriophage PhiYe-F10 Lysis Spectrum and Analysis of the Relationship between Lysis Ability and Virulence Gene of Yersinia Enterocolitica]

To determine the lysis spectrum of Yersinia enterocolitica bacteriophage phiYe-F10 and to analyze the relationship between the lysis ability of phiYe-F10 and the virulence gene of Yersinia enterocolitica. To observe the lysis ability of the phage phiYe-F10 to the different Yersinia strains with the double-layer technique. The strains used in this study including 213 of Yersinia enterocolitica and 36 of Yersinia pseudotuberculosis and 1 of Yersinia pestis. The virulence genes of these Yersinia enterocolitica (attachment invasion locus (ail) and enterotoxin (ystA, ystB) and yersinia adhesin A (yadA), virulence factor (virF), specific gene for lipopolysaccharide O-side chain of serotype O : 3 (rfbc) were all detected. Among the 213 Yersinia enterocolitica, 84 strains were O : 3 serotype (78 strains with rfbc gene), 10 were serotype O : 5, 13 were serotype O : 8, 34 were serotype O : 9 and 72 were other serotypes. Of these, 77 were typical pathogenic Yersinia enterocolitica harboring with virulence plasmid (ail+, ystA+, ystB-, yadA+, virF+), and 15 were pathogenic bacterial strains deficiency virulence plasmid (ail+, ystA+, ystB-, yadA-, virF-) and the rest 121 were non pathogenic genotype strains. PhiYe-F10 lysed the 71 serotype O : 3 Yersinia enterocolitica strains which were all carried with rfbc+, including 52 pathogenic Yersinia enterocolitica, 19 nonpathogenic Y. enterocolitica. The phiYe-F10 can not lysed serotype O : 5, O : 9 and other serotype Y. enterocolitica, the lysis rate of serotype O : 3 was as high as 84.5%. The phiYe-F10 can not lysed Yersinia pseudotuberculosis and Yersinia pestis. Yersinia phage phiYe-F10 is highly specific for serotype O : 3 Yersinia enterocolitic at 25 degrees C, which showed a typical narrow lysis spectrum. Phage phiYe-F10 can lysed much more pathogenic Y. enterocolitica than nonpathogenic Y. enterocolitica.

Investigating light-use efficiency across a jack pine chronosequence during dry and wet years

Light-use efficiency (LUE) is the ability of vegetated canopies to use light for photosynthesis. Together with remote sensing estimates of canopy cover and meteorological inputs, LUE provides a physical basis for scaling carbon uptake processes from the stand to the global scale. A better understanding of the factors that control LUE will result in improved global estimates of carbon uptake from the terrestrial biosphere. To examine factors that control variability in LUE in stands of different ages during dry and wet conditions, we measured LUE in a chronosequence of four jack pine stands (recent clearcut (age 1-3), regenerating (age 8-9), immature (age 29-30) and mature (approximately 90 years old)) during one normal (2002), one very dry (2003) and two very wet (2004, 2005) growing seasons in Saskatchewan, Canada. Cumulative CO(2) fluxes decreased significantly at all sites during the drought year of 2003, as did mean LUE. Canopy foliage at the recently regenerating jack pine site increased by 19% between 2002 and 2003. Foliage growth rate was reduced by 6% between 2003 and 2004, and foliage biomass decreased by 6% from 2004 to 2005. Over the four years studied, LUE was greatest at the mature jack pine site and lower, but similar, at the other three sites. Mean growing-season LUE varied with mean soil water content at each site, except at that of the newly regenerating stand where soil water had little influence. Mean daily vapor pressure deficit typically had the greatest influence on variability in LUE at all sites. Diffuse versus direct radiation also had significant but varying effects on LUE in jack pine stands of different ages.

Effects of elevated carbon dioxide concentration and temperature on needle growth, respiration and carbohydrate status in field-grown Scots pines during the needle expansion period

We determined effects of long-term elevation of carbon dioxide concentration ([CO2]) and temperature on growth, respiration and carbohydrate concentration in needles of field-grown Scots pine (Pinus sylvestris L.) trees during the needle expansion period. Sixteen 20-year-old Scots pine trees were individually enclosed in closed-top, environmentally controlled chambers for 4 years in one of four environments: ambient conditions (CON); elevated [CO2] (EC); elevated temperature (ET); and a combination of both (EC + ET). Needle growth, carbohydrate concentration and dark respiration were measured at 3-day intervals throughout the needle expansion period. Dark respiration was partitioned into growth and maintenance components by regressing specific respiration rate against specific growth rate. In all treatments, growth, carbohydrate concentration and daily dark respiration rates of needles followed a similar seasonal pattern throughout the needle expansion period. Treatments EC, ET and EC + ET increased individual needle area and dry weight compared with the CON treatment. Carbohydrate concentrations in needles were increased by EC, but reduced by ET and EC + ET. Daily respiration rates increased slightly in the early stage of needle expansion and decreased gradually in the late stage when needles were exposed to EC, but increased consistently throughout the growing period when needles were exposed to ET or EC + ET. Partitioning of respiration into its two functional components showed that the growth respiration coefficient was unaffected by the treatments, whereas maintenance respiration was reduced by EC but increased by ET and EC + ET. Maintenance respiration was more sensitive to elevated temperature than growth respiration. We conclude that the difference in respiration rates between expanding and expanded needles should be taken into account when estimating the respiratory responses of needles to elevated [CO2] and temperature.